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Rama Ranganathan - Publications

Affiliations: 
1997-2017 University of Texas Southwestern Medical Center, Dallas, TX, United States 
 2017- Biochemistry and Molecular Biology University of Chicago, Chicago, IL 
Website:
https://newfaculty.uchicago.edu/page/rama-ranganathan
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58 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Kleeorin Y, Russ WP, Rivoire O, Ranganathan R. Undersampling and the inference of coevolution in proteins. Cell Systems. PMID 36693377 DOI: 10.1016/j.cels.2022.12.013  0.346
2020 Walker AS, Russ WP, Ranganathan R, Schepartz A. RNA sectors and allosteric function within the ribosome. Proceedings of the National Academy of Sciences of the United States of America. PMID 32747536 DOI: 10.1073/pnas.1909634117  0.386
2020 Russ WP, Figliuzzi M, Stocker C, Barrat-Charlaix P, Socolich M, Kast P, Hilvert D, Monasson R, Cocco S, Weigt M, Ranganathan R. An evolution-based model for designing chorismate mutase enzymes. Science (New York, N.Y.). 369: 440-445. PMID 32703877 DOI: 10.1126/Science.Aba3304  0.368
2020 Kim JS, McGough L, Klyshko E, Ranganathan R, Rauscher S. Novel Simulation Methods for Electric Field-Induced Dynamics of Protein Crystals Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.902  0.304
2020 Klyshko E, McGough L, Kim JS, Ranganathan R, Rauscher S. EF-X in Silico - Modeling Protein Dynamics in an Electric Field Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.2778  0.316
2019 Poelwijk FJ, Socolich M, Ranganathan R. Learning the pattern of epistasis linking genotype and phenotype in a protein. Nature Communications. 10: 4213. PMID 31527666 DOI: 10.1038/s41467-019-12130-8  0.373
2019 Ranganathan R, Sela I, Wheeler L. Decision letter: ASPEN, a methodology for reconstructing protein evolution with improved accuracy using ensemble models Elife. DOI: 10.7554/Elife.47676.026  0.301
2019 Hekstra D, Lee BR, Dalton KM, Ranganathan R. Analysis of electric-field stimulated time-resolved X-ray crystallography data Acta Crystallographica Section A. 75. DOI: 10.1107/S0108767319096077  0.699
2018 Creixell P, Pandey JP, Palmeri A, Bhattacharyya M, Creixell M, Ranganathan R, Pincus D, Yaffe MB. Hierarchical Organization Endows the Kinase Domain with Regulatory Plasticity. Cell Systems. PMID 30243563 DOI: 10.1016/J.Cels.2018.08.008  0.344
2018 Ranganathan R, Salinas VH. Coevolution-based inference of amino acid interactions underlying protein function. Elife. 7. PMID 30024376 DOI: 10.7554/eLife.34300  0.434
2018 Rosensweig C, Reynolds KA, Gao P, Laothamatas I, Shan Y, Ranganathan R, Takahashi JS, Green CB. An evolutionary hotspot defines functional differences between CRYPTOCHROMES. Nature Communications. 9: 1138. PMID 29556064 DOI: 10.1038/S41467-018-03503-6  0.694
2018 Salinas VH, Ranganathan R. Author response: Coevolution-based inference of amino acid interactions underlying protein function Elife. DOI: 10.7554/Elife.34300.029  0.384
2017 Bandaru P, Shah NH, Bhattacharyya M, Barton JP, Kondo Y, Cofsky JC, Gee CL, Chakraborty AK, Kortemme T, Ranganathan R, Kuriyan J. Deconstruction of the Ras switching cycle through saturation mutagenesis. Elife. 6. PMID 28686159 DOI: 10.7554/Elife.27810  0.334
2016 Hekstra DR, White KI, Socolich MA, Henning RW, Šrajer V, Ranganathan R. Electric-field-stimulated protein mechanics. Nature. PMID 27926732 DOI: 10.1038/Nature20571  0.758
2016 Shah NH, Wang Q, Yan Q, Karandur D, Kadlecek TA, Fallahee IR, Russ WP, Ranganathan R, Weiss A, Kuriyan J. An electrostatic selection mechanism controls sequential kinase signaling downstream of the T cell receptor. Elife. 5. PMID 27700984 DOI: 10.7554/Elife.20105  0.327
2016 Stiffler MA, Subramanian SK, Salinas VH, Ranganathan R. A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing. Journal of Visualized Experiments : Jove. PMID 27403811 DOI: 10.3791/54119  0.375
2016 Poelwijk FJ, Krishna V, Ranganathan R. The Context-Dependence of Mutations: A Linkage of Formalisms. Plos Computational Biology. 12: e1004771. PMID 27337695 DOI: 10.1371/journal.pcbi.1004771  0.328
2016 Raman AS, White KI, Ranganathan R. Origins of Allostery and Evolvability in Proteins: A Case Study. Cell. PMID 27321669 DOI: 10.1016/j.cell.2016.05.047  0.419
2016 Rivoire O, Reynolds KA, Ranganathan R. Evolution-Based Functional Decomposition of Proteins. Plos Computational Biology. 12: e1004817. PMID 27254668 DOI: 10.1371/Journal.Pcbi.1004817  0.73
2016 Mangelsdorf D, Ranganathan R. Alfred Goodman Gilman (1941–2015) Cell. 164: 589-590. DOI: 10.1016/J.CELL.2016.01.042  0.324
2015 Stiffler MA, Hekstra DR, Ranganathan R. Evolvability as a function of purifying selection in TEM-1 β-lactamase. Cell. 160: 882-92. PMID 25723163 DOI: 10.1016/J.Cell.2015.01.035  0.723
2014 Ma L, Ranganathan R. Systems-level characterization of the kernel mechanism of the cyanobacterial circadian oscillator. Bio Systems. 117: 30-9. PMID 24444761 DOI: 10.1016/j.biosystems.2014.01.002  0.307
2013 Reynolds KA, Russ WP, Socolich M, Ranganathan R. Evolution-based design of proteins. Methods in Enzymology. 523: 213-35. PMID 23422432 DOI: 10.1016/B978-0-12-394292-0.00010-2  0.71
2012 McLaughlin RN, Poelwijk FJ, Raman A, Gosal WS, Ranganathan R. The spatial architecture of protein function and adaptation. Nature. 491: 138-42. PMID 23041932 DOI: 10.1038/nature11500  0.436
2012 Ma L, Ranganathan R. Quantifying the rhythm of KaiB-C interaction for in vitro cyanobacterial circadian clock. Plos One. 7: e42581. PMID 22900029 DOI: 10.1371/journal.pone.0042581  0.352
2011 Reynolds KA, McLaughlin RN, Ranganathan R. Hot spots for allosteric regulation on protein surfaces. Cell. 147: 1564-75. PMID 22196731 DOI: 10.1016/J.Cell.2011.10.049  0.704
2010 Smock RG, Rivoire O, Russ WP, Swain JF, Leibler S, Ranganathan R, Gierasch LM. An interdomain sector mediating allostery in Hsp70 molecular chaperones. Molecular Systems Biology. 6: 414. PMID 20865007 DOI: 10.1038/Msb.2010.65  0.666
2010 Levine B, Ranganathan R. Autophagy: Snapshot of the network. Nature. 466: 38-40. PMID 20596005 DOI: 10.1038/466038a  0.407
2009 Halabi N, Rivoire O, Leibler S, Ranganathan R. Protein sectors: evolutionary units of three-dimensional structure. Cell. 138: 774-86. PMID 19703402 DOI: 10.1016/J.Cell.2009.07.038  0.669
2008 Lee J, Natarajan M, Nashine VC, Socolich M, Vo T, Russ WP, Benkovic SJ, Ranganathan R. Surface sites for engineering allosteric control in proteins. Science (New York, N.Y.). 322: 438-42. PMID 18927392 DOI: 10.1126/Science.1159052  0.465
2008 Pumir A, Graves J, Ranganathan R, Shraiman BI. Systems analysis of the single photon response in invertebrate photoreceptors. Proceedings of the National Academy of Sciences of the United States of America. 105: 10354-9. PMID 18653755 DOI: 10.1073/Pnas.0711884105  0.375
2007 Ranganathan R. Biochemistry. Signaling across the cell membrane. Science (New York, N.Y.). 318: 1253-4. PMID 18033872 DOI: 10.1126/science.1151656  0.394
2007 Mishra P, Socolich M, Wall MA, Graves J, Wang Z, Ranganathan R. Dynamic scaffolding in a G protein-coupled signaling system. Cell. 131: 80-92. PMID 17923089 DOI: 10.1016/j.cell.2007.07.037  0.375
2007 Ferguson AD, Amezcua CA, Halabi NM, Chelliah Y, Rosen MK, Ranganathan R, Deisenhofer J. Signal transduction pathway of TonB-dependent transporters. Proceedings of the National Academy of Sciences of the United States of America. 104: 513-8. PMID 17197416 DOI: 10.1073/Pnas.0609887104  0.368
2006 Poole AM, Ranganathan R. Knowledge-based potentials in protein design. Current Opinion in Structural Biology. 16: 508-13. PMID 16843652 DOI: 10.1016/j.sbi.2006.06.013  0.427
2006 Natarajan M, Lin KM, Hsueh RC, Sternweis PC, Ranganathan R. A global analysis of cross-talk in a mammalian cellular signalling network. Nature Cell Biology. 8: 571-80. PMID 16699502 DOI: 10.1038/Ncb1418  0.37
2005 Russ WP, Lowery DM, Mishra P, Yaffe MB, Ranganathan R. Natural-like function in artificial WW domains. Nature. 437: 579-83. PMID 16177795 DOI: 10.1038/Nature03990  0.412
2005 Socolich M, Lockless SW, Russ WP, Lee H, Gardner KH, Ranganathan R. Evolutionary information for specifying a protein fold. Nature. 437: 512-8. PMID 16177782 DOI: 10.1038/Nature03991  0.731
2004 Shulman AI, Larson C, Mangelsdorf DJ, Ranganathan R. Structural determinants of allosteric ligand activation in RXR heterodimers. Cell. 116: 417-29. PMID 15016376 DOI: 10.1016/S0092-8674(04)00119-9  0.401
2004 Jain RK, Ranganathan R. Local complexity of amino acid interactions in a protein core. Proceedings of the National Academy of Sciences of the United States of America. 101: 111-6. PMID 14684834 DOI: 10.1073/pnas.2534352100  0.438
2003 Hatley ME, Lockless SW, Gibson SK, Gilman AG, Ranganathan R. Allosteric determinants in guanine nucleotide-binding proteins. Proceedings of the National Academy of Sciences of the United States of America. 100: 14445-50. PMID 14623969 DOI: 10.1073/Pnas.1835919100  0.746
2003 Süel GM, Lockless SW, Wall MA, Ranganathan R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nature Structural Biology. 10: 59-69. PMID 12483203 DOI: 10.1038/Nsb881  0.793
2003 Süel GM, Lockless SW, Wall MA, Ranganathan R. Erratum: Evolutionarily conserved networks of residues mediate allosteric communication in proteins Nature Structural & Molecular Biology. 10: 232-232. DOI: 10.1038/Nsb0303-232  0.763
2002 Russ WP, Ranganathan R. Knowledge-based potential functions in protein design. Current Opinion in Structural Biology. 12: 447-52. PMID 12163066 DOI: 10.1016/S0959-440X(02)00346-9  0.438
2000 Wall MA, Socolich M, Ranganathan R. The structural basis for red fluorescence in the tetrameric GFP homolog DsRed. Nature Structural Biology. 7: 1133-8. PMID 11101896 DOI: 10.1038/81992  0.373
2000 Kiselev A, Socolich M, Vinós J, Hardy RW, Zuker CS, Ranganathan R. A molecular pathway for light-dependent photoreceptor apoptosis in Drosophila. Neuron. 28: 139-52. PMID 11086990 DOI: 10.1016/S0896-6273(00)00092-1  0.75
1999 Lockless SW, Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science (New York, N.Y.). 286: 295-9. PMID 10514373 DOI: 10.1126/science.286.5438.295  0.751
1999 Zuker CS, Ranganathan R. The path to specificity. Science (New York, N.Y.). 283: 650-1. PMID 9988659 DOI: 10.1126/Science.283.5402.650  0.632
1997 Ranganathan R, Ross EM. PDZ domain proteins: scaffolds for signaling complexes. Current Biology : Cb. 7: R770-3. PMID 9382826 DOI: 10.1016/S0960-9822(06)00401-5  0.394
1997 Ranganathan R, Lu KP, Hunter T, Noel JP. Structural and functional analysis of the mitotic rotamase Pin1 suggests substrate recognition is phosphorylation dependent. Cell. 89: 875-86. PMID 9200606 DOI: 10.1016/S0092-8674(00)80273-1  0.56
1996 Ranganathan R, Lewis JH, MacKinnon R. Spatial localization of the K+ channel selectivity filter by mutant cycle-based structure analysis. Neuron. 16: 131-9. PMID 8562077 DOI: 10.1016/S0896-6273(00)80030-6  0.473
1995 Ranganathan R, Stevens CF. Arrestin binding determines the rate of inactivation of the G protein-coupled receptor rhodopsin in vivo. Cell. 81: 841-8. PMID 7781061 DOI: 10.1016/0092-8674(95)90004-7  0.383
1995 Ranganathan R, Malicki DM, Zuker CS. Signal transduction in Drosophila photoreceptors. Annual Review of Neuroscience. 18: 283-317. PMID 7605064 DOI: 10.1146/annurev.ne.18.030195.001435  0.726
1994 Ranganathan R, Bacskai BJ, Tsien RY, Zuker CS. Cytosolic calcium transients: spatial localization and role in Drosophila photoreceptor cell function. Neuron. 13: 837-48. PMID 7946332 DOI: 10.1016/0896-6273(94)90250-X  0.569
1993 Dolph PJ, Ranganathan R, Colley NJ, Hardy RW, Socolich M, Zuker CS. Arrestin function in inactivation of G protein-coupled receptor rhodopsin in vivo. Science (New York, N.Y.). 260: 1910-6. PMID 8316831 DOI: 10.1126/Science.8316831  0.772
1991 Smith DP, Ranganathan R, Hardy RW, Marx J, Tsuchida T, Zuker CS. Photoreceptor deactivation and retinal degeneration mediated by a photoreceptor-specific protein kinase C. Science (New York, N.Y.). 254: 1478-84. PMID 1962207 DOI: 10.1126/Science.1962207  0.629
1991 Ranganathan R, Harris GL, Stevens CF, Zuker CS. A Drosophila mutant defective in extracellular calcium-dependent photoreceptor deactivation and rapid desensitization. Nature. 354: 230-2. PMID 1961249 DOI: 10.1038/354230a0  0.624
1991 Ranganathan R, Harris WA, Zuker CS. The molecular genetics of invertebrate phototransduction. Trends in Neurosciences. 14: 486-93. PMID 1726765 DOI: 10.1016/0166-2236(91)90060-8  0.63
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